Job ID = 16432814 SRX = SRX10274853 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 21556302 spots for SRR13895159/SRR13895159.sra Written 21556302 spots for SRR13895159/SRR13895159.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434122 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:11 21556302 reads; of these: 21556302 (100.00%) were unpaired; of these: 592787 (2.75%) aligned 0 times 17360849 (80.54%) aligned exactly 1 time 3602666 (16.71%) aligned >1 times 97.25% overall alignment rate Time searching: 00:09:11 Overall time: 00:09:11 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 3875193 / 20963515 = 0.1849 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 09:49:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10274853/SRX10274853.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10274853/SRX10274853.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10274853/SRX10274853.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10274853/SRX10274853.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 02 Aug 2022 09:49:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:49:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:50:01: 1000000 INFO @ Tue, 02 Aug 2022 09:50:11: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 09:50:21: 3000000 INFO @ Tue, 02 Aug 2022 09:50:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10274853/SRX10274853.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10274853/SRX10274853.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10274853/SRX10274853.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10274853/SRX10274853.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 02 Aug 2022 09:50:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:50:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:50:31: 4000000 INFO @ Tue, 02 Aug 2022 09:50:32: 1000000 INFO @ Tue, 02 Aug 2022 09:50:40: 5000000 INFO @ Tue, 02 Aug 2022 09:50:42: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 09:50:51: 6000000 INFO @ Tue, 02 Aug 2022 09:50:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10274853/SRX10274853.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10274853/SRX10274853.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10274853/SRX10274853.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10274853/SRX10274853.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 02 Aug 2022 09:50:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:50:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:50:53: 3000000 INFO @ Tue, 02 Aug 2022 09:51:01: 7000000 INFO @ Tue, 02 Aug 2022 09:51:03: 4000000 INFO @ Tue, 02 Aug 2022 09:51:04: 1000000 INFO @ Tue, 02 Aug 2022 09:51:13: 8000000 INFO @ Tue, 02 Aug 2022 09:51:15: 5000000 INFO @ Tue, 02 Aug 2022 09:51:16: 2000000 INFO @ Tue, 02 Aug 2022 09:51:24: 9000000 INFO @ Tue, 02 Aug 2022 09:51:25: 6000000 INFO @ Tue, 02 Aug 2022 09:51:29: 3000000 INFO @ Tue, 02 Aug 2022 09:51:34: 10000000 INFO @ Tue, 02 Aug 2022 09:51:36: 7000000 INFO @ Tue, 02 Aug 2022 09:51:42: 4000000 INFO @ Tue, 02 Aug 2022 09:51:44: 11000000 INFO @ Tue, 02 Aug 2022 09:51:47: 8000000 INFO @ Tue, 02 Aug 2022 09:51:54: 5000000 INFO @ Tue, 02 Aug 2022 09:51:55: 12000000 INFO @ Tue, 02 Aug 2022 09:52:00: 9000000 INFO @ Tue, 02 Aug 2022 09:52:05: 13000000 INFO @ Tue, 02 Aug 2022 09:52:06: 6000000 INFO @ Tue, 02 Aug 2022 09:52:13: 10000000 INFO @ Tue, 02 Aug 2022 09:52:16: 14000000 INFO @ Tue, 02 Aug 2022 09:52:18: 7000000 INFO @ Tue, 02 Aug 2022 09:52:23: 11000000 INFO @ Tue, 02 Aug 2022 09:52:26: 15000000 INFO @ Tue, 02 Aug 2022 09:52:29: 8000000 INFO @ Tue, 02 Aug 2022 09:52:33: 12000000 INFO @ Tue, 02 Aug 2022 09:52:36: 16000000 INFO @ Tue, 02 Aug 2022 09:52:41: 9000000 INFO @ Tue, 02 Aug 2022 09:52:43: 13000000 INFO @ Tue, 02 Aug 2022 09:52:46: 17000000 INFO @ Tue, 02 Aug 2022 09:52:47: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 09:52:47: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 09:52:47: #1 total tags in treatment: 17088322 INFO @ Tue, 02 Aug 2022 09:52:47: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:52:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 09:52:47: #1 tags after filtering in treatment: 17088322 INFO @ Tue, 02 Aug 2022 09:52:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:52:47: #1 finished! INFO @ Tue, 02 Aug 2022 09:52:47: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:52:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:52:48: #2 number of paired peaks: 296 WARNING @ Tue, 02 Aug 2022 09:52:48: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Tue, 02 Aug 2022 09:52:48: start model_add_line... INFO @ Tue, 02 Aug 2022 09:52:48: start X-correlation... INFO @ Tue, 02 Aug 2022 09:52:48: end of X-cor INFO @ Tue, 02 Aug 2022 09:52:48: #2 finished! INFO @ Tue, 02 Aug 2022 09:52:48: #2 predicted fragment length is 97 bps INFO @ Tue, 02 Aug 2022 09:52:48: #2 alternative fragment length(s) may be 3,97 bps INFO @ Tue, 02 Aug 2022 09:52:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10274853/SRX10274853.05_model.r WARNING @ Tue, 02 Aug 2022 09:52:48: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 09:52:48: #2 You may need to consider one of the other alternative d(s): 3,97 WARNING @ Tue, 02 Aug 2022 09:52:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 09:52:48: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:52:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:52:52: 14000000 INFO @ Tue, 02 Aug 2022 09:52:52: 10000000 INFO @ Tue, 02 Aug 2022 09:53:02: 15000000 INFO @ Tue, 02 Aug 2022 09:53:04: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 09:53:15: 16000000 INFO @ Tue, 02 Aug 2022 09:53:17: 12000000 INFO @ Tue, 02 Aug 2022 09:53:23: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:53:26: 17000000 INFO @ Tue, 02 Aug 2022 09:53:27: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 09:53:27: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 09:53:27: #1 total tags in treatment: 17088322 INFO @ Tue, 02 Aug 2022 09:53:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:53:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 09:53:27: #1 tags after filtering in treatment: 17088322 INFO @ Tue, 02 Aug 2022 09:53:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:53:27: #1 finished! INFO @ Tue, 02 Aug 2022 09:53:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:53:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:53:28: 13000000 INFO @ Tue, 02 Aug 2022 09:53:28: #2 number of paired peaks: 296 WARNING @ Tue, 02 Aug 2022 09:53:28: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Tue, 02 Aug 2022 09:53:28: start model_add_line... INFO @ Tue, 02 Aug 2022 09:53:29: start X-correlation... INFO @ Tue, 02 Aug 2022 09:53:29: end of X-cor INFO @ Tue, 02 Aug 2022 09:53:29: #2 finished! INFO @ Tue, 02 Aug 2022 09:53:29: #2 predicted fragment length is 97 bps INFO @ Tue, 02 Aug 2022 09:53:29: #2 alternative fragment length(s) may be 3,97 bps INFO @ Tue, 02 Aug 2022 09:53:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10274853/SRX10274853.10_model.r WARNING @ Tue, 02 Aug 2022 09:53:29: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 09:53:29: #2 You may need to consider one of the other alternative d(s): 3,97 WARNING @ Tue, 02 Aug 2022 09:53:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 09:53:29: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:53:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:53:37: 14000000 INFO @ Tue, 02 Aug 2022 09:53:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10274853/SRX10274853.05_peaks.xls INFO @ Tue, 02 Aug 2022 09:53:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10274853/SRX10274853.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:53:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10274853/SRX10274853.05_summits.bed INFO @ Tue, 02 Aug 2022 09:53:41: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (8336 records, 4 fields): 60 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:53:46: 15000000 INFO @ Tue, 02 Aug 2022 09:53:55: 16000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 09:54:02: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:54:03: 17000000 INFO @ Tue, 02 Aug 2022 09:54:04: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 09:54:04: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 09:54:04: #1 total tags in treatment: 17088322 INFO @ Tue, 02 Aug 2022 09:54:04: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:54:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 09:54:04: #1 tags after filtering in treatment: 17088322 INFO @ Tue, 02 Aug 2022 09:54:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:54:04: #1 finished! INFO @ Tue, 02 Aug 2022 09:54:04: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:54:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:54:06: #2 number of paired peaks: 296 WARNING @ Tue, 02 Aug 2022 09:54:06: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Tue, 02 Aug 2022 09:54:06: start model_add_line... INFO @ Tue, 02 Aug 2022 09:54:06: start X-correlation... INFO @ Tue, 02 Aug 2022 09:54:06: end of X-cor INFO @ Tue, 02 Aug 2022 09:54:06: #2 finished! INFO @ Tue, 02 Aug 2022 09:54:06: #2 predicted fragment length is 97 bps INFO @ Tue, 02 Aug 2022 09:54:06: #2 alternative fragment length(s) may be 3,97 bps INFO @ Tue, 02 Aug 2022 09:54:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10274853/SRX10274853.20_model.r WARNING @ Tue, 02 Aug 2022 09:54:06: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 09:54:06: #2 You may need to consider one of the other alternative d(s): 3,97 WARNING @ Tue, 02 Aug 2022 09:54:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 09:54:06: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:54:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:54:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10274853/SRX10274853.10_peaks.xls INFO @ Tue, 02 Aug 2022 09:54:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10274853/SRX10274853.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:54:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10274853/SRX10274853.10_summits.bed INFO @ Tue, 02 Aug 2022 09:54:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2871 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:54:39: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:54:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10274853/SRX10274853.20_peaks.xls INFO @ Tue, 02 Aug 2022 09:54:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10274853/SRX10274853.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:54:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10274853/SRX10274853.20_summits.bed INFO @ Tue, 02 Aug 2022 09:54:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (633 records, 4 fields): 24 millis CompletedMACS2peakCalling